Structure of PDB 4rd6 Chain A Binding Site BS01

Receptor Information
>4rd6 Chain A (length=405) Species: 273057 (Saccharolobus solfataricus P2) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AWPKVQPEVNIGVVGHVDHGKTTLVQAITGIWTSKHSKLGYAETNIGVCE
SCKKPEAYVTEPSCKSCGSDDEPKFLRRISFIDAPGHEVLMATMLSGAAL
MDGAILVVAANEPFPQPQTREHFVALGIIGVKNLIIVQNKVDVVSKEEAL
SQYRQIKQFTKGTWAENVPIIPVSALHKINIDSLIEGIEEYIKTPYRDLS
QKPVMLVIRSFDVNKPGTQFNELKGGVIGGSIIQGLFKVDQEIKVLPGLR
VEKQGKVSYEPIFTKISSIRFGDEEFKEAKPGGLVAIGTYLDPSLTKADN
LLGSIITLADAEVPVLWNIRIKYNLLERVVGAKEMLKVDPIRAKETLMLS
VGSSTTLGIVTSVKKDEIEVELRRPVAVWSNNIRTVISRQIAGRWRMIGW
GLVEI
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain4rd6 Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4rd6 Identification of a second GTP-bound magnesium ion in archaeal initiation factor 2.
Resolution1.944 Å
Binding residue
(original residue number in PDB)		D19 G21 K22 T23 T24 N149 K150 D152 S184 L186
Binding residue
(residue number reindexed from 1)		D18 G20 K21 T22 T23 N139 K140 D142 S174 L176
Annotation score4
Binding affinityMOAD: Kd=0.52uM
PDBbind-CN: -logKd/Ki=6.28,Kd=0.52uM
Enzymatic activity
Catalytic site (original residue number in PDB) D19 K22 T23 H97
Catalytic site (residue number reindexed from 1) D18 K21 T22 H87
Enzyme Commision number 3.6.5.3: protein-synthesizing GTPase.
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0003743 translation initiation factor activity
GO:0003746 translation elongation factor activity
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
Biological Process
GO:0001731 formation of translation preinitiation complex
GO:0006412 translation
GO:0006413 translational initiation
GO:0006414 translational elongation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4rd6, PDBe:4rd6, PDBj:4rd6
PDBsum4rd6
PubMed25690901
UniProtQ980A5|IF2G_SACS2 Translation initiation factor 2 subunit gamma (Gene Name=eif2g)

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